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Tuesday, November 20, 2012

The body's response to fasting, part 1: proteins

I apologize to those of you who already understand all this thoroughly, but judging from my conversations with Noel, it seems like the best plan is for me to start with basics. And no, the irony of writing a series of posts on fasting during the Thanksgiving/Winter Festival of Your Choice/New Year season is not lost on me.

I sat and stared at my screen for quite some time just now, because there are several ways I could launch into this. After much deliberation, I've decided to jump in with proteins, because almost everything that goes on in our bodies has a protein behind it. Considering the variety of activities that go on in our bodies, it might be surprising to find out that one family of molecules is behind all of it. This is because proteins are polymers - large molecules constructed by stringing together smaller molecular units. In the case of proteins, these units are amino acids.

The great thing about amino acids is that part of the molecule is the same for every amino acid (called the backbone), and part of it varies from molecule to molecule (called a side chain). The backbone is the part that gets linked to other amino acids. Because that part is the same for all of them, they all get linked together the same way. The side chain determines what chemical properties the amino acid has, and therefore what chemical properties the protein will have. The proteins that they comprise are huge - hundreds or even thousands of amino acids linked together. So as you can probably imagine, it's a difficult task figuring out how the properties of all these individual amino acids come together to produce the chemical properties of the whole protein. It's something we're still working on figuring out, but we're gradually making headway.

The huge size of proteins makes them very sensitive to their environment. Each amino acid side chain is like a little feeler, interacting with the surrounding water and salts and sugars and other proteins and all the other molecules that are floating around in their body. Each side chain (or group of side chains that end up next to each other in the protein structure) is attracted to certain molecules and repelled by others.

To make things even more interesting, amino acid side chain within the same protein interact with each other. So every protein has a distinct shape. Many of them have dense cores at the center of the structure. They form grooves and pockets that are well suited to housing certain molecules. They form long fibers. They form protruding knobs that can latch onto other molecules. They form things shaped like hairpins. So many different shapes!

Ready for things to get really interesting? The sensitivity of proteins to their environment combines with their tendency to make distinct shapes to create distinct shapes that can change depending on the specific environment! Emergent properties, baby! Have I mentioned that I love biochemistry? It blows my mind!

Ok, now that I've gone over why proteins are not only important but also amazing, my plan for next time is to get into gene expression and how proteins are involved in that. However, if there's something that's still a little fuzzy from this post that you'd like me to go over in a little more detail instead, let me know. Likewise, if you already understand gene expression just fine, thank you very much, and you'd like me to pick up the pace a little bit, you can let me know that, too.

Let the late fall/early winter festivities commence! But don't get too carried away, because your proteins are watching you ...